Mercurial > repos > melissacline > ucsc_xena_platform
annotate xena_utils.py @ 44:da86478b1d64
clean up strange tools that just a url linkout
| author | jingchunzhu <jingchunzhu@gmail.com> |
|---|---|
| date | Mon, 27 Jul 2015 15:30:10 -0700 |
| parents | d64a002c3b0c |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 """ | |
| 3 xenaUtils: a set of python utilities for the Galaxy / Xena interface | |
| 4 """ | |
| 5 | |
| 6 import os | |
| 7 import socket | |
| 8 import subprocess | |
|
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a3fbe077a14c
replace wget with python method
jingchunzhu <jingchunzhu@gmail.com>
parents:
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9 import httplib |
| 0 | 10 |
| 11 def jarPath(): | |
| 12 """Return the full pathname of the xena jar file""" | |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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13 jarPath = os.getenv('XENA_JAR_PATH', "~") |
| 0 | 14 return(os.path.join(jarPath, "xena.jar")) |
| 15 | |
| 16 | |
| 17 def baseDir(): | |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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18 return(os.getenv('XENA_BASE_DIR', "/tmp")) |
| 0 | 19 |
| 20 def fileDir(): | |
| 21 return(baseDir() + "/files") | |
| 22 | |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
0
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23 def hostname(): |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
0
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24 hostname = subprocess.check_output("hostname -f", shell=True).rstrip() |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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25 return hostname |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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26 |
| 0 | 27 def isRunning(xenaPort): |
| 28 """Determine if Xena is running on the specified port""" | |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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29 |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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30 host = hostname() |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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31 try: |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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32 httpServ = httplib.HTTPConnection(host, xenaPort) |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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33 httpServ.connect() |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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34 |
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jingchunzhu <jingchunzhu@gmail.com>
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35 data = "(+ 1 2)" |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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36 httpServ.request('POST', '/data/', data) |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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37 response = httpServ.getresponse() |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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38 if response.status == httplib.OK: |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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39 content = response.read() |
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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40 except: |
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jingchunzhu <jingchunzhu@gmail.com>
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41 return False |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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42 |
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a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
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43 return (content == "3.0") |
| 0 | 44 |
| 45 def findUnusedPort(): | |
| 46 """Find a random port that is available on the local system, and return | |
| 47 the port number. | |
| 48 """ | |
| 49 ss = socket.socket(socket.AF_INET, socket.SOCK_STREAM) | |
| 50 ss.bind(('', 0)) | |
| 51 portNumber = ss.getsockname()[1] | |
| 52 ss.close() | |
| 53 return(portNumber) | |
| 54 | |
| 55 def isPortAvailable(port): | |
| 56 """Test if a given port is available""" | |
| 57 ss = socket.socket(socket.AF_INET, socket.SOCK_STREAM) | |
| 58 try: | |
| 59 ss.bind(('', port)) | |
| 60 except: | |
| 61 return False | |
| 62 else: | |
| 63 ss.close() | |
| 64 return True | |
| 65 | |
| 66 def portFilename(): | |
| 67 """ Return the name of the file with the port of the running Xena, | |
| 68 if any | |
| 69 """ | |
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34
a3fbe077a14c
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jingchunzhu <jingchunzhu@gmail.com>
parents:
0
diff
changeset
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70 xenaBaseDir = os.getenv('XENA_BASE_DIR', "~") |
| 0 | 71 xenaPortFilename = xenaBaseDir + "/xena.port" |
| 72 return(xenaPortFilename) | |
| 73 | |
| 74 def port(testIfAvailable=False, findNewPort=False): | |
| 75 preferredXenaPort = 7220 | |
| 76 xenaPort = None | |
| 77 xenaPortFname = portFilename() | |
| 78 if os.path.exists(xenaPortFname): | |
| 79 fp = open(xenaPortFname) | |
| 80 line = fp.readline() | |
| 81 xenaPort = int(line.rstrip()) | |
| 82 if testIfAvailable and not isRunning(xenaPort): | |
| 83 # Xena is not running on the port. Make sure that | |
| 84 # the port is not occupied by some other process | |
| 85 if not isPortAvailable(xenaPort): | |
| 86 #cmd = "lsof -t -i :%s -sTCP:LISTEN" % portID | |
| 87 #pid = subprocess.check_output(cmd, shell=True).rstrip() | |
| 88 #print "not available, used by",pid | |
| 89 xenaPort = None | |
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34
a3fbe077a14c
replace wget with python method
jingchunzhu <jingchunzhu@gmail.com>
parents:
0
diff
changeset
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90 |
| 0 | 91 if findNewPort and xenaPort == None: |
| 92 if isPortAvailable(preferredXenaPort): | |
| 93 xenaPort = preferredXenaPort | |
| 94 else: | |
| 95 xenaPort = findUnusedPort() | |
| 96 fp = open(portFilename(), "w") | |
| 97 fp.write("%d\n" % xenaPort) | |
| 98 fp.close() | |
| 99 return(xenaPort) | |
| 100 | |
| 101 def cleanUpPort(): | |
| 102 """ Clean up the port file after Xena has stopped running""" | |
| 103 os.unlink(portFilename()) | |
| 104 | |
| 105 | |
| 106 |